Single‐cell RNA‐seq reveals fate determination control of an individual fibre cell initiation in cotton (Gossypium hirsutum)

Plant Biotechnology Journal, Год журнала: 2022, Номер 20(12), С. 2372 - 2388

Опубликована: Авг. 29, 2022

Summary Cotton fibre is a unicellular seed trichome, and lint initials per as factor determines yield. However, the mechanisms controlling initiation from ovule epidermis are not understood well enough. Here, with single‐cell RNA sequencing (scRNA‐seq), total of 14 535 cells were identified cotton outer integument Xu142_LF line at four developmental stages (1.5, 1, 0.5 days before anthesis day anthesis). Three major cell types, fibre, non‐fibre pigment layer then verified by in situ hybridization. A comparative analysis on scRNA‐seq data between Xu142 its fibreless mutant fl further confirmed cluster definition. The trajectory was reconstructed, differentiated 1 anthesis. Gene regulatory networks revealed spatiotemporal pattern core transcription factors, MYB25‐like HOX3 demonstrated played key roles commanders differentiation tip‐biased diffuse growth respectively. model for early development single proposed here, which sheds light deciphering mechanism plant trichome improvement

Язык: Английский

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Environmental control of rice flowering time

Plant Communications, Год журнала: 2023, Номер 4(5), С. 100610 - 100610

Опубликована: Май 4, 2023

Correct measurement of environmental parameters is fundamental for plant fitness and survival, as well timing developmental transitions, including the switch from vegetative to reproductive growth. Important that affect flowering time include day length (photoperiod) temperature. Their response pathways have been best described in Arabidopsis, which currently offers a detailed conceptual framework serves comparison other species. Rice, focus this review, also possesses photoperiodic pathway, but 150 million years divergent evolution very different environments diversified its molecular architecture. The ambient temperature perception pathway strongly intertwined with photoperiod essentially converges on same genes modify time. When observing network topologies, it evident rice centered EARLY HEADING DATE 1, rice-specific transcriptional regulator. Here, we summarize most important features network, an emphasis uniqueness, discuss connections hormonal, perception, stress pathways.

Язык: Английский

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Asymmetric gene expression and cell-type-specific regulatory networks in the root of bread wheat revealed by single-cell multiomics analysis

Genome biology, Год журнала: 2023, Номер 24(1)

Опубликована: Апрель 4, 2023

Homoeologs are defined as homologous genes resulting from allopolyploidy. Bread wheat, Triticum aestivum, is an allohexaploid species with many homoeologs. Homoeolog expression bias, referring to the relative contribution of homoeologs transcriptome, critical for determining traits that influence wheat growth and development. Asymmetric transcription has been so far investigated in a tissue or organ-specific manner, which could be misleading due mixture cell types.

Язык: Английский

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Single-cell transcriptomic analysis reveals the developmental trajectory and transcriptional regulatory networks of pigment glands in Gossypium bickii

Molecular Plant, Год журнала: 2023, Номер 16(4), С. 694 - 708

Опубликована: Фев. 10, 2023

Comprehensive utilization of cottonseeds is limited by the presence pigment glands and its inclusion gossypol. The ideal cotton has glandless seeds but a glanded plant, trait found in only few Australian wild species, including Gossypium bickii. Introgression this into cultivated species proved to be difficult. Understanding biological processes toward gland morphogenesis associated underlying molecular mechanisms will facilitate breeding varieties with plant. In study, single-cell RNA sequencing (scRNA-seq) was performed on 12 222 protoplasts isolated from cotyledons germinating G. bickii 48 h after imbibition. Clustered 14 distinct clusters unsupervisedly, these cells could grouped eight cell populations assistance known marker genes. were well separated others parenchyma cells, secretory apoptotic cells. By integrating developmental trajectory, transcription factor regulatory networks, core functional validation, we established model for formation. model, light gibberellin verified promote formation glands. addition, three novel genes, GbiERF114 (ETHYLENE RESPONSE FACTOR 114), GbiZAT11 (ZINC FINGER OF ARABIDOPSIS THALIANA 11), GbiNTL9 (NAC TRANSCRIPTION FACTOR-LIKE 9), affect Collectively, findings provide new insights lay cornerstone future scRNA-seq investigations.

Язык: Английский

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Best practices for the execution, analysis, and data storage of plant single-cell/nucleus transcriptomics

The Plant Cell, Год журнала: 2024, Номер 36(4), С. 812 - 828

Опубликована: Янв. 17, 2024

Abstract Single-cell and single-nucleus RNA-sequencing technologies capture the expression of plant genes at an unprecedented resolution. Therefore, these are gaining traction in molecular developmental biology for elucidating transcriptional changes across cell types a specific tissue or organ, upon treatments, response to biotic abiotic stresses, between genotypes. Despite rapidly accelerating use technologies, collective standardized experimental analytical procedures support acquisition high-quality data sets still missing. In this commentary, we discuss common challenges associated with single-cell transcriptomics plants propose general guidelines improve reproducibility, quality, comparability, interpretation make readily available community fast-developing field research.

Язык: Английский

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Orthologous marker groups reveal broad cell identity conservation across plant single-cell transcriptomes

Nature Communications, Год журнала: 2025, Номер 16(1)

Опубликована: Янв. 2, 2025

Single-cell RNA sequencing (scRNA-seq) is widely used in plant biology and a powerful tool for studying cell identity differentiation. However, the scarcity of known cell-type marker genes divergence expression patterns limit accuracy identification our capacity to investigate conservation many species. To tackle this challenge, we devise novel computational strategy called Orthologous Marker Gene Groups (OMGs), which can identify types both model non-model species allows rapid comparison across published single-cell maps. Our method does not require cross-species data integration, while still accurately determining inter-species cellular similarities. We validate by analyzing from with well-annotated maps, show methods capture majority manually annotated types. The robustness further demonstrated its ability pertinently map clusters 1 million cells, 268 15 diverse reveal 14 dominant groups substantial shared markers monocots dicots. facilitate use broad research community, launch user-friendly web-based OMG browser, simplifies process datasets biologists. A Ortho-Marker (OMGs) was developed enable single data. revealed conserved accessible via browser.

Язык: Английский

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Single‐Cell RNA Sequencing Reveals the Developmental Landscape of Wheat Roots

Plant Cell & Environment, Год журнала: 2025, Номер unknown

Опубликована: Янв. 6, 2025

Allohexaploid wheat (Triticum aestivum L.) is one of the major crops worldwide, however there very limited research on transcriptional programmes underlying cell type specification. Single-cell RNA sequencing (scRNA-seq) was used to unravel transcriptome heterogeneity cells and composition types in broad-spectrum organisms. Here, we reported scRNA-seq transcriptomes single from root tips Chinese spring (CS) cultivar, defined cell-type-specific marker genes, identified most types. We further profiled reconstructed developmental trajectories stem niche (SCN), proximal meristems meristems, unveiled gene expression signature water transportation, divulged asymmetric transcription subgenomes explored evolutionary conservation divergence cultivar rice (Nip 93-11, ZH11) through interspecies comparison. Collectively, this work underscored landscape roots provided a single-cell perspective for differentiation trajectory application, unbalanced pattern characteristics between two plant species, contributing better understanding development at unprecedented resolution.

Язык: Английский

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Mass spectrometry imaging and single-cell transcriptional profiling reveal the tissue-specific regulation of bioactive ingredient biosynthesis in Taxus leaves

Plant Communications, Год журнала: 2023, Номер 4(5), С. 100630 - 100630

Опубликована: Май 25, 2023

Taxus leaves provide the raw industrial materials for taxol, a natural antineoplastic drug widely used in treatment of various cancers. However, precise distribution, biosynthesis, and transcriptional regulation taxoids other active components remain unknown. Matrix-assisted laser desorption/ionization-mass spectrometry imaging analysis was to visualize secondary metabolites leaf sections mairei, confirming tissue-specific accumulation different metabolites. Single-cell sequencing produce expression profiles 8846 cells, with median 2352 genes per cell. Based on series cluster-specific markers, cells were grouped into 15 clusters, suggesting high degree cell heterogeneity T. mairei leaves. Our data create first metabolic single-cell atlas reveal spatial temporal patterns several pathways. According cell-type annotation, most taxol biosynthesis are expressed mainly mesophyll cells; phenolic acid flavonoid highly epidermal (including stomatal complex guard cells); terpenoid steroid specifically cells. A number novel cell-specific transcription factors involved metabolite identified, including MYB17, WRKY12, WRKY31, ERF13, GT_2, bHLH46. research establishes landscape major types at resolution provides valuable resources studying basic principles cell-type-specific metabolism.

Язык: Английский

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Integrated mass spectrometry imaging and single‐cell transcriptome atlas strategies provide novel insights into taxoid biosynthesis and transport in Taxus mairei stems

The Plant Journal, Год журнала: 2023, Номер 115(5), С. 1243 - 1260

Опубликована: Май 23, 2023

Taxol, which is a widely used important chemotherapeutic agent, was originally isolated from Taxus stem barks. However, little known about the precise distribution of taxoids and transcriptional regulation taxoid biosynthesis across stems. Here, we MALDI-IMS analysis to visualize mairei stems single-cell RNA sequencing generate expression profiles. A T. atlas created, providing spatial pattern cells. Cells were reordered using main developmental pseudotime trajectory provided temporal patterns in Most taxol biosynthesis-related genes primarily expressed epidermal, endodermal, xylem parenchyma cells, caused an uneven We developed strategy screen novel transcription factors (TFs) involved regulation. Several TF genes, such as endodermal cell-specific MYB47 NAC2 bHLH68, implicated potential regulators biosynthesis. Furthermore, ATP-binding cassette family transporter gene, ABCG2, proposed candidate. In summary, generated metabolic identified molecular mechanisms underpinning pathway.

Язык: Английский

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Advances in the Application of Single-Cell Transcriptomics in Plant Systems and Synthetic Biology

BioDesign Research, Год журнала: 2024, Номер 6, С. 0029 - 0029

Опубликована: Янв. 1, 2024

Plants are complex systems hierarchically organized and composed of various cell types. To understand the molecular underpinnings plant systems, single-cell RNA sequencing (scRNA-seq) has emerged as a powerful tool for revealing high resolution gene expression patterns at cellular level investigating cell-type heterogeneity. Furthermore, scRNA-seq analysis biosystems great potential generating new knowledge to inform design synthetic biology, which aims modify plants genetically/epigenetically through genome editing, engineering, or re-writing based on rational increasing crop yield quality, promoting bioeconomy enhancing environmental sustainability. In particular, data from studies can be utilized facilitate development high-precision Build-Design-Test-Learn capabilities maximizing targeted performance engineered while minimizing unintended side effects. date, been demonstrated in limited number species, including model (e.g., Arabidopsis thaliana), agricultural crops Oryza sativa), bioenergy Populus spp.). It is expected that future technical advancements will reduce cost consequently accelerate application this emerging technology plants. review, we summarize current scRNA-seq, sample preparation, sequencing, analysis, provide guidance how choose appropriate methods different types samples. We then highlight applications both biology research. Finally, discuss challenges opportunities

Язык: Английский

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